Born in Edinburgh, he was a nephew of Lachlan Macpherson, 17th Chief of the Clan. He went to sea as a boy and by age 31 he had become master of the 21-gun privateer, Britannia of Philadelphia which raided French merchant ships during the Seven Years War (1754-1763). In the process he lost his arm in battle and acquired enough wealth to build Mount Pleasant, the mansion that still graces Fairmont Park in modern Philadelphia.

      By the time of the Revolution he had become thoroughly American and was employed as a secret agent by the Continental Congress, although he applied for command of the Continental Navy. Congress sent him to Cambridge with a plan to burn the British Navy in Boston Harbour, but Washington rejected this scheme. Later on, he published an article in which he claimed that he entered the Hessian lines near Trenton as a spy and was responsible for information that led to Washington's victory there. Be that as it may, Captain Macpherson did serve his adopted country well by totally funding the construction of five Continental men-of-war which he presented to the Pennsylvania Navy.

      His two sons served as officers in the Continental Army. John, the eldest was killed in the assault on Quebec City on New Year's Eve 1775 and William, who had served in the British Army before the Revolution from the age of 14. After resigning his commission he joined the American ranks in which he served with distinction as a major. William later served in the Pennsylvania legislature during which time he voted for adoption of the US Constitution. He also served long as Surveyor of Customs for the Port of Philadelphia and as a Brigadier General of the Pennsylvania Militia during the Whiskey Rebellion of 1791.

      After the Revolution Captain John undertook service to the public in a more peaceful vein lecturing on astronomy and natural philosophy, publishing the first trade paper in the country, the Price-Current and creating the first city directory in the USA. He was also an inventor, if not as practical a one, and equally busy with the arts and with pamphleteering, writing what he called "comic tragedies" for the stage, and indulging in insulting controversies with eminent men such that at one time he was imprisoned for three months as being insane. Finally, in 1789, he published an auto-biography, the cover of which is seen below. Only 48 pages of that work have survived and now reside in the US Library of Congress.